# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 19:14:19 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (4S)-2-{(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl}-5-methylidene-5,6-dihydro-4H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](NC(=O)Cc1sccc1)C2=N[C@H](C(O)=O)C(=C)CS2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 THN  THN  '(4S)-2-{(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl}-5-methylidene-5,6-dihydro-4H-1,3-thiazine-4-carboxylic acid'  ligand  37  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_THN
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 THN  S1    S  S2    0   0.083   0.0656   1.4788  -1.7676
 THN  C2    C  CH2   0  -0.619  -0.5877   1.7404  -3.4508
 THN  C3    C  C     0   0.146  -1.4629   0.6057  -3.8616
 THN  C3'   C  C2    0  -0.555  -2.7282   0.7696  -4.2273
 THN  C4    C  CH1   0  -0.300  -0.8184  -0.7570  -3.8128
 THN  C4'   C  C     0   0.552   0.3055  -0.8165  -4.8410
 THN  O4A   O  OH1   0  -0.579  -0.1763  -0.9439  -6.0658
 THN  O4B   O  O     0  -0.415   1.4723  -0.7212  -4.5708
 THN  N5    N  N     0  -0.316  -0.2878  -1.1318  -2.5252
 THN  C6    C  C     0   0.081   0.0836  -0.2785  -1.6777
 THN  C7    C  CH1   0  -0.220   0.6212  -0.7893  -0.3516
 THN  C8    C  C     0   0.537   2.0992  -0.4151  -0.2477
 THN  O9A   O  O     0  -0.421   2.9573  -1.0634  -0.7852
 THN  O9B   O  OH1   0  -0.573   2.3039   0.6961   0.4304
 THN  N10   N  NH1   0  -0.653  -0.1739  -0.2923   0.7384
 THN  C11   C  C     0   0.590   0.0716  -0.7084   1.9941
 THN  O12   O  O     0  -0.472   1.0038  -1.4487   2.2566
 THN  C13   C  CH2   0  -0.648  -0.9134  -0.2326   3.0404
 THN  C14   C  CR5   0  -0.133  -0.2849   0.0858   4.3547
 THN  C15   C  CR15  0  -0.235  -0.4508   1.2262   5.0839
 THN  C16   C  CR15  0  -0.187   0.2304   1.1971   6.3316
 THN  C17   C  CR15  0  -0.476   0.8972   0.0280   6.5299
 THN  S19   S  S2    0   0.220   0.7170  -1.0352   5.1968
 THN  H21   H  HCH2  0   0.308   0.2633   1.8688  -4.1212
 THN  H22   H  HCH2  0   0.317  -1.1372   2.6794  -3.4183
 THN  H3'1  H  H     0   0.259  -3.1881   1.7491  -4.2504
 THN  H3'2  H  H     0   0.260  -3.3436  -0.0683  -4.5292
 THN  H4    H  HCH1  0   0.313  -1.5629  -1.5088  -4.0859
 THN  HO4   H  HOH1  0   0.488   0.5456  -0.9338  -6.7125
 THN  H7    H  HCH1  0   0.327   0.5745  -1.8789  -0.4062
 THN  HO9   H  HOH1  0   0.490   3.2485   0.9146   0.4378
 THN  H10   H  HNH1  0   0.417  -0.9634   0.3059   0.5493
 THN  H131  H  HCH2  0   0.287  -1.4611   0.6436   2.6917
 THN  H132  H  HCH2  0   0.308  -1.6539  -1.0326   3.1539
 THN  H15   H  HCR5  0   0.261  -1.0485   2.0598   4.7406
 THN  H16   H  HCR5  0   0.264   0.2249   2.0108   7.0423
 THN  H17   H  HCR5  0   0.291   1.5048  -0.2557   7.3756

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 THN  S1   C2    single    1.824  0.020  1.824
 THN  S1   C6    single    1.760  0.020  1.760
 THN  C2   C3    single    1.491  0.020  1.491
 THN  C2   H21   single    0.970  0.020  1.090
 THN  C2   H22   single    0.970  0.020  1.090
 THN  C3   C3'   double    1.327  0.020  1.327
 THN  C3   C4    single    1.508  0.020  1.508
 THN  C3'  H3'1  single    0.930  0.020  1.080
 THN  C3'  H3'2  single    0.930  0.020  1.080
 THN  C4   C4'   single    1.525  0.020  1.525
 THN  C4   N5    single    1.442  0.020  1.442
 THN  C4   H4    single    0.970  0.020  1.090
 THN  C4'  O4A   single    1.322  0.020  1.322
 THN  C4'  O4B   double    1.201  0.020  1.201
 THN  O4A  HO4   single    0.850  0.020  0.980
 THN  N5   C6    double    1.259  0.020  1.259
 THN  C6   C7    single    1.519  0.020  1.519
 THN  C7   C8    single    1.528  0.020  1.528
 THN  C7   N10   single    1.438  0.020  1.438
 THN  C7   H7    single    0.970  0.020  1.090
 THN  C8   O9A   double    1.202  0.020  1.202
 THN  C8   O9B   single    1.318  0.020  1.318
 THN  O9B  HO9   single    0.850  0.020  0.980
 THN  N10  C11   single    1.345  0.020  1.345
 THN  N10  H10   single    0.860  0.020  1.020
 THN  C11  O12   double    1.219  0.020  1.219
 THN  C11  C13   single    1.514  0.020  1.514
 THN  C13  C14   single    1.491  0.020  1.491
 THN  C13  H131  single    0.970  0.020  1.090
 THN  C13  H132  single    0.970  0.020  1.090
 THN  C14  C15   aromatic  1.364  0.020  1.364
 THN  C14  S19   aromatic  1.723  0.020  1.723
 THN  C15  C16   aromatic  1.422  0.020  1.422
 THN  C15  H15   single    0.930  0.020  1.080
 THN  C16  C17   aromatic  1.360  0.020  1.360
 THN  C16  H16   single    0.930  0.020  1.080
 THN  C17  S19   aromatic  1.715  0.020  1.715
 THN  C17  H17   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 THN  C6    S1   C2    101.19  3.000
 THN  H22   C2   H21   108.10  3.000
 THN  H22   C2   C3    111.62  3.000
 THN  H21   C2   C3    112.22  3.000
 THN  H22   C2   S1    106.08  3.000
 THN  H21   C2   S1    107.73  3.000
 THN  C3    C2   S1    110.81  3.000
 THN  C4    C3   C3'   121.86  3.000
 THN  C4    C3   C2    115.34  3.000
 THN  C3'   C3   C2    122.80  3.000
 THN  H3'2  C3'  H3'1  116.93  3.000
 THN  H3'2  C3'  C3    121.55  3.000
 THN  H3'1  C3'  C3    121.51  3.000
 THN  H4    C4   N5    107.16  3.000
 THN  H4    C4   C4'   107.87  3.000
 THN  N5    C4   C4'   108.71  3.000
 THN  H4    C4   C3    108.81  3.000
 THN  N5    C4   C3    114.89  3.000
 THN  C4'   C4   C3    109.17  3.000
 THN  O4B   C4'  O4A   124.74  3.000
 THN  O4B   C4'  C4    124.14  3.000
 THN  O4A   C4'  C4    111.09  3.000
 THN  HO4   O4A  C4'   110.22  3.000
 THN  C6    N5   C4    122.25  3.000
 THN  C7    C6   N5    117.66  3.000
 THN  C7    C6   S1    112.58  3.000
 THN  N5    C6   S1    129.76  3.000
 THN  H7    C7   N10   111.04  3.000
 THN  H7    C7   C8    106.80  3.000
 THN  N10   C7   C8    113.49  3.000
 THN  H7    C7   C6    106.06  3.000
 THN  N10   C7   C6    110.48  3.000
 THN  C8    C7   C6    108.62  3.000
 THN  O9B   C8   O9A   125.02  3.000
 THN  O9B   C8   C7    113.06  3.000
 THN  O9A   C8   C7    121.86  3.000
 THN  HO9   O9B  C8    110.20  3.000
 THN  H10   N10  C11   120.09  3.000
 THN  H10   N10  C7    119.72  3.000
 THN  C11   N10  C7    119.99  3.000
 THN  C13   C11  O12   122.66  3.000
 THN  C13   C11  N10   115.41  3.000
 THN  O12   C11  N10   121.89  3.000
 THN  H132  C13  H131  106.28  3.000
 THN  H132  C13  C14   110.45  3.000
 THN  H131  C13  C14   108.78  3.000
 THN  H132  C13  C11   106.37  3.000
 THN  H131  C13  C11   110.99  3.000
 THN  C14   C13  C11   113.71  3.000
 THN  S19   C14  C15   110.70  3.000
 THN  S19   C14  C13   122.46  3.000
 THN  C15   C14  C13   126.77  3.000
 THN  H15   C15  C16   123.99  3.000
 THN  H15   C15  C14   122.82  3.000
 THN  C16   C15  C14   113.19  3.000
 THN  H16   C16  C17   123.64  3.000
 THN  H16   C16  C15   124.01  3.000
 THN  C17   C16  C15   112.35  3.000
 THN  H17   C17  S19   120.36  3.000
 THN  H17   C17  C16   128.03  3.000
 THN  S19   C17  C16   111.60  3.000
 THN  C17   S19  C14    92.16  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 THN  CONST_01  C17   C16  C15  C14     0.00   0.0  0
 THN  CONST_02  C16   C17  S19  C14     0.00   0.0  0
 THN  CONST_03  C17   S19  C14  C15     0.00   0.0  0
 THN  CONST_04  S19   C17  C16  C15     0.00   0.0  0
 THN  CONST_05  S19   C14  C15  C16     0.00   0.0  0
 THN  CONST_06  C16   C15  C14  C13   180.00   0.0  0
 THN  CONST_07  C17   S19  C14  C13   180.00   0.0  0
 THN  CONST_08  H16   C16  C15  C14   180.00   0.0  0
 THN  CONST_09  H17   C17  S19  C14   180.00   0.0  0
 THN  CONST_10  H15   C15  C16  C17   180.00   0.0  0
 THN  CONST_11  HO4   O4A  C4'  C4    180.00   0.0  0
 THN  CONST_12  O12   C11  N10  C7      0.00   0.0  0
 THN  CONST_13  C13   C11  N10  C7    180.00   0.0  0
 THN  CONST_14  H10   N10  C11  O12   180.00   0.0  0
 THN  CONST_15  HO9   O9B  C8   C7    180.00   0.0  0
 THN  Var_01    C4    C3   C2   S1    -56.64  30.0  1
 THN  Var_02    N5    C6   S1   C2     -1.82  30.0  1
 THN  Var_03    C15   C14  C13  C11   129.94  30.0  2
 THN  Var_04    H3'1  C3'  C3   C2      0.39  30.0  2
 THN  Var_05    C14   C13  C11  N10  -143.05  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 THN  chir_01  C4  C3   C4'  N5  negativ
 THN  chir_02  C7  N10  C8   C6  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 THN  plan-1  C13  0.020
 THN  plan-1  C14  0.020
 THN  plan-1  C15  0.020
 THN  plan-1  C16  0.020
 THN  plan-1  C17  0.020
 THN  plan-1  S19  0.020
 THN  plan-1  H15  0.020
 THN  plan-1  H16  0.020
 THN  plan-1  H17  0.020
 THN  plan-2  C7   0.020
 THN  plan-2  N10  0.020
 THN  plan-2  C11  0.020
 THN  plan-2  O12  0.020
 THN  plan-2  C13  0.020
 THN  plan-2  H10  0.020
 THN  plan-3  C4   0.020
 THN  plan-3  C4'  0.020
 THN  plan-3  O4A  0.020
 THN  plan-3  O4B  0.020
 THN  plan-3  HO4  0.020
 THN  plan-4  C7   0.020
 THN  plan-4  C8   0.020
 THN  plan-4  O9A  0.020
 THN  plan-4  O9B  0.020
 THN  plan-4  HO9  0.020

